Package index • chronogram

Assemble a chronogram & add data

cg_assemble(): Assemble a chronogram

cg_add_experiment(): Add experimental data to a chronogram

cg_add_treatment(): Add treatment data to a chronogram

Annotate a chronogram

Episode annotation

Find episodes from results (tests, symptoms) on different calendar days

cg_annotate_episodes_find(): Find infections per individual

cg_annotate_episodes_find_seroconversion(): Find seroconversion episodes per individual

cg_annotate_episodes_fill(): Fill experimental, treatment or symptom information within an infection episode

Episode, vaccine & exposure counting

cg_annotate_episodes_count(): Calculate and assign flags based on infection history

cg_annotate_vaccines_count(): Calculate and assign flags based on vaccine history

cg_annotate_exposures_count(): Cumulative counting seroconversion episodes per individual

cg_annotate_antigenic_history(): Calculate and assign flags based on infection history

Filter, window & select a chronogram

cg_window_by_episode(): Pick a window of dates from a chronogram: with respect to episode start.

cg_window_by_metadata(): Pick a window before and after a metadata date column

cg_window_by_visit(): Pick a window of dates from a chronogram: with respect to visits.

cg_select(): Adapted dplyr::select() to include calendar dates and ID columns

cg_select_visit(): Select a visit within a windowed chronogram

IO

Save and load a chronogram

cg_save(): Save a chronogram

cg_load(): Load a chronogram

Example datasets

smallstudy: Small study

built_smallstudy: Small study: pre-built chronogram

pitch_chronogram: PITCH study: pre-built chronogram

Plots

Visualise chronogram using ggplot2

cg_plot(): cg_plot

cg_plot_meta(): cg_plot_meta

chronogram class

S3 constructor, helper and validator functions

chronogram(): Build a chronogram, from a chronogram_skeleton and metadata

chronogram_skeleton(): Build a chronogram skeleton, a two column index of IDs and calendar dates, a scaffold for a chronogram

new_grouped_chronogram(): New grouped chronogram

new_tbl2chronogram(): new_tbl2chronogram

check_experiment(): check ExperimentalData

check_metadata(): check metadata

validate_chronogram(): Validate chronogram

validate_chronogram_skeleton(): validate chronogram skeleton

Extending dplyr, tibble

dplyr_row_slice(<cg_tbl>) dplyr_col_modify(<cg_tbl>) dplyr_reconstruct(<cg_tbl>) dplyr_row_slice(<grouped_cg_df>) group_data_trim() dplyr_col_modify(<grouped_cg_df>) dplyr_reconstruct(<grouped_cg_df>): Extending dplyr to chronogram

group_by(<cg_tbl>) ungroup(<grouped_cg_df>): group-by & ungroup-by chronogram

glimpse(<cg_tbl>): Glimpse S3 method for chronogram objects (class cg_tbl)

glimpse(<grouped_cg_df>): Glimpse S3 method for grouped chronogram objects (class grouped_cg_df)

glimpse_experiment_data(): Glimpse S3 method for experiment data from chronogram objects (class cg_tbl)

glimpse_metadata(): Glimpse S3 method for metadata from chronogram objects (class cg_tbl)